RNPH_MYCTU
ID RNPH_MYCTU Reviewed; 259 AA.
AC P9WGZ7; L0T9C5; Q10628;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 40.
DE RecName: Full=Ribonuclease PH {ECO:0000255|HAMAP-Rule:MF_00564};
DE Short=RNase PH {ECO:0000255|HAMAP-Rule:MF_00564};
DE EC=2.7.7.56 {ECO:0000255|HAMAP-Rule:MF_00564};
DE AltName: Full=tRNA nucleotidyltransferase {ECO:0000255|HAMAP-Rule:MF_00564};
GN Name=rph {ECO:0000255|HAMAP-Rule:MF_00564}; Synonyms=rphA;
GN OrderedLocusNames=Rv1340; ORFNames=MTCY02B10.04, MTCY130.25;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [3] {ECO:0007744|PDB:3B4T}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 2-259 IN COMPLEX WITH SUBSTRATE,
RP AND SUBUNIT.
RA Antczak A.J., Lekin T., Segelke B.W., Berger J.M.;
RT "2.1 A crystal structure of RNase PH from Mycobacterium tuberculosis.";
RL Submitted (OCT-2007) to the PDB data bank.
CC -!- FUNCTION: Phosphorolytic 3'-5' exoribonuclease that plays an important
CC role in tRNA 3'-end maturation. Removes nucleotide residues following
CC the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of
CC RNA molecules by using nucleoside diphosphates as substrates, but this
CC may not be physiologically important. Probably plays a role in
CC initiation of 16S rRNA degradation (leading to ribosome degradation)
CC during starvation. {ECO:0000255|HAMAP-Rule:MF_00564}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=phosphate + tRNA(n+1) = a ribonucleoside 5'-diphosphate +
CC tRNA(n); Xref=Rhea:RHEA:10628, Rhea:RHEA-COMP:17343, Rhea:RHEA-
CC COMP:17344, ChEBI:CHEBI:43474, ChEBI:CHEBI:57930, ChEBI:CHEBI:173114;
CC EC=2.7.7.56; Evidence={ECO:0000255|HAMAP-Rule:MF_00564};
CC -!- SUBUNIT: Homohexameric ring arranged as a trimer of dimers (Ref.3).
CC {ECO:0000255|HAMAP-Rule:MF_00564, ECO:0000305|Ref.3}.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000255|HAMAP-
CC Rule:MF_00564}.
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DR EMBL; AL123456; CCP44098.1; -; Genomic_DNA.
DR PIR; C70739; C70739.
DR RefSeq; NP_215856.1; NC_000962.3.
DR RefSeq; WP_003406926.1; NZ_NVQJ01000031.1.
DR PDB; 3B4T; X-ray; 2.10 A; A/B/C/D/E/F=2-259.
DR PDBsum; 3B4T; -.
DR AlphaFoldDB; P9WGZ7; -.
DR SMR; P9WGZ7; -.
DR STRING; 83332.Rv1340; -.
DR PaxDb; P9WGZ7; -.
DR DNASU; 886864; -.
DR GeneID; 886864; -.
DR KEGG; mtu:Rv1340; -.
DR TubercuList; Rv1340; -.
DR eggNOG; COG2123; Bacteria.
DR OMA; KGKGQGW; -.
DR PhylomeDB; P9WGZ7; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009022; F:tRNA nucleotidyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0016075; P:rRNA catabolic process; IBA:GO_Central.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-UniRule.
DR CDD; cd11362; RNase_PH_bact; 1.
DR Gene3D; 3.30.230.70; -; 1.
DR HAMAP; MF_00564; RNase_PH; 1.
DR InterPro; IPR001247; ExoRNase_PH_dom1.
DR InterPro; IPR015847; ExoRNase_PH_dom2.
DR InterPro; IPR036345; ExoRNase_PH_dom2_sf.
DR InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR002381; RNase_PH_bac-type.
DR InterPro; IPR018336; RNase_PH_CS.
DR Pfam; PF01138; RNase_PH; 1.
DR Pfam; PF03725; RNase_PH_C; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55666; SSF55666; 1.
DR TIGRFAMs; TIGR01966; RNasePH; 1.
DR PROSITE; PS01277; RIBONUCLEASE_PH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Nucleotidyltransferase; Reference proteome; RNA-binding;
KW rRNA processing; Transferase; tRNA processing; tRNA-binding.
FT CHAIN 1..259
FT /note="Ribonuclease PH"
FT /id="PRO_0000139912"
FT BINDING 88
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00564"
FT BINDING 126..128
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00564,
FT ECO:0000305|Ref.3"
FT STRAND 16..20
FT /evidence="ECO:0007829|PDB:3B4T"
FT STRAND 22..34
FT /evidence="ECO:0007829|PDB:3B4T"
FT STRAND 37..48
FT /evidence="ECO:0007829|PDB:3B4T"
FT STRAND 60..67
FT /evidence="ECO:0007829|PDB:3B4T"
FT HELIX 69..71
FT /evidence="ECO:0007829|PDB:3B4T"
FT STRAND 72..74
FT /evidence="ECO:0007829|PDB:3B4T"
FT HELIX 79..82
FT /evidence="ECO:0007829|PDB:3B4T"
FT HELIX 87..101
FT /evidence="ECO:0007829|PDB:3B4T"
FT HELIX 106..109
FT /evidence="ECO:0007829|PDB:3B4T"
FT STRAND 111..122
FT /evidence="ECO:0007829|PDB:3B4T"
FT HELIX 127..148
FT /evidence="ECO:0007829|PDB:3B4T"
FT STRAND 153..155
FT /evidence="ECO:0007829|PDB:3B4T"
FT STRAND 162..170
FT /evidence="ECO:0007829|PDB:3B4T"
FT STRAND 173..177
FT /evidence="ECO:0007829|PDB:3B4T"
FT HELIX 180..183
FT /evidence="ECO:0007829|PDB:3B4T"
FT STRAND 187..195
FT /evidence="ECO:0007829|PDB:3B4T"
FT STRAND 200..205
FT /evidence="ECO:0007829|PDB:3B4T"
FT HELIX 214..239
FT /evidence="ECO:0007829|PDB:3B4T"
SQ SEQUENCE 259 AA; 27351 MW; D8461B3089929F9F CRC64;
MSKREDGRLD HELRPVIITR GFTENPAGSV LIEFGHTKVL CTASVTEGVP RWRKATGLGW
LTAEYAMLPS ATHSRSDRES VRGRLSGRTQ EISRLIGRSL RACIDLAALG ENTIAIDCDV
LQADGGTRTA AITGAYVALA DAVTYLSAAG KLSDPRPLSC AIAAVSVGVV DGRIRVDLPY
EEDSRAEVDM NVVATDTGTL VEIQGTGEGA TFARSTLDKL LDMALGACDT LFAAQRDALA
LPYPGVLPQG PPPPKAFGT
